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Molecular fluids undergoing shear flow are often modeled using a homogeneous nonequilibrium molecular dynamics algorithm. To reach a steady state, this method must be used in conjunction with a thermostating mechanism which duplicates the heat dissipation in the experimental setup (e.g., by conduction to the shearing boundaries). The most commonly used type of thermostat involves fixing the center of mass kinetic (c.m.) temperature. Though perfectly valid, this approach does not seem to be the...[Show more] most realistic for a molecular fluid since heat is removed only through the 3 degrees of freedom of the center of mass for each molecule. The second type of thermostat involves fixing the “atomic” kinetic temperature and therefore takes into account all degrees of freedom. However, since the streaming velocity of atoms within their constituent molecules is unknown, the implementation of such a thermostat is problematic and relies on incorrect assumptions on the streaming velocity of atoms. The recently developed configurational temperature thermostat requires no assumption on the streaming velocity of atoms and takes into account all degrees of freedom. Using a configurational temperature thermostat to thermostat homogeneous shear flow thus seems to be a more realistic approach than the c.m. kinetic thermostat. In this work, we apply this configurational temperature thermostat to the study of linear alkanes (C₁₀ and C₂₀) undergoing shear flow. The results so obtained are compared with those obtained using a c.m. kinetic thermostat. Our aims are (1) to test the influence of the total number of degrees of freedom of the system, (2) to make a connection between the results obtained with the two types of thermostats. By carefully examining the energies of the internal modes, we have been able to characterize the loss of accuracy of a c.m. kinetic thermostat at high shear rates and for high molecular weight compounds. Finally, we establish a correspondence between the two types of thermostats by showing that, for the internal modes, a simulation at a fixed c.m. kinetic temperature is equivalent to a simulation at a fixed but higher configurational temperature.